Publications

Evan Seitz, David McCandlish, Justin Kinney, Peter Koo (2025). Uncovering the Mechanistic Landscape of Regulatory DNA with Deep Learning. bioRxiv.

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Evan Seitz, David McCandlish, Justin Kinney, Peter Koo (2025). Decoding the Mechanistic Impact of Genetic Variation on Regulatory Sequences with Deep Learning. ICLR GEM Workshop.

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Evan Seitz, David McCandlish, Justin Kinney, Peter Koo (2024). Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models. Nat Mach Intell.

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Evan Seitz, Joachim Frank, Peter Schwander (2023). Beyond ManifoldEM: Geometric relationships between manifold embeddings of a continuum of 3D molecular structures and their 2D projections. R. Soc. Chem. Digital Discovery.

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Evan Seitz, Francisco Acosta-Reyes, Suvrajit Maji, Peter Schwander, Joachim Frank (2022). Recovery of conformational continuum from single-particle cryo-EM images: Optimization of ManifoldEM informed by ground truth. IEEE TCI.

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Evan Seitz (2022). Analysis of Conformational Continuum and Free-energy Landscapes from Manifold Embedding of Single-particle Cryo-EM Ensembles of Biomolecules. Columbia University Libraries.

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Evan Seitz, Francisco Acosta-Reyes, Suvrajit Maji, Peter Schwander, Joachim Frank (2021). Geometric machine learning informed by ground truth: Recovery of conformational continuum from single-particle cryo-EM data of biomolecules. bioRxiv.

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Terra Sztain, Surl-Hee Ahn, Anthony Bogetti, Lorenzo Casalino, Jory Goldsmith, Evan Seitz, Ryan McCool, Fiona Kearns, Francisco Acosta-Reyes, Suvrajit Maji, Ghoncheh Mashayekhi, Andrew McCammon, Abbas Ourmazd, Joachim Frank, Jason McLellan, Lillian Chong, Rommie Amaro (2021). A glycan gate controls opening of the SARS-CoV-2 spike protein. Nat. Chem.

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Evan Seitz, Joachim Frank (2020). POLARIS: Path of least action analysis on energy landscapes. J. Chem. Inf. Model.

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Evan Seitz, Francisco Acosta-Reyes, Peter Schwander, Joachim Frank (2019). Simulation of cryo-EM ensembles from atomic models of molecules exhibiting continuous conformations. bioRxiv.

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